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    XAGE3 X antigen family member 3 [ Homo sapiens (human) ]

    Gene ID: 170626, updated on 27-Nov-2024

    Summary

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    Official Symbol
    XAGE3provided by HGNC
    Official Full Name
    X antigen family member 3provided by HGNC
    Primary source
    HGNC:HGNC:14618
    See related
    Ensembl:ENSG00000171402 MIM:300740; AllianceGenome:HGNC:14618
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PLAC6; GAGED4; XAGE-3; pp9012; CT12.3a; CT12.3b
    Summary
    This gene is a member of the XAGE subfamily, which belongs to the GAGE family. The GAGE genes are expressed in a variety of tumors and in some fetal and reproductive tissues. This gene is expressed in placenta and fetal liver/spleen, and may function in inhibiting cancer cell growth. The protein encoded by this gene shares a sequence similarity with other GAGE/PAGE proteins. Because of the expression pattern and the sequence similarity, this protein also belongs to a family of CT (cancer-testis) antigens. Alternative splicing of this gene generates 2 transcript variants differing in the 5' UTR. [provided by RefSeq, Jul 2008]
    Expression
    Restricted expression toward placenta (RPKM 81.9) See more
    Orthologs
    all
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    Genomic context

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    See XAGE3 in Genome Data Viewer
    Location:
    Xp11.22
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (52862528..52868083, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (52147439..52153059, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (52891557..52897114, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene X antigen family member 3-like Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:52855217-52856182 Neighboring gene eukaryotic translation initiation factor 4A2 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29644 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:52895119-52896318 Neighboring gene family with sequence similarity 156 member B Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:52949629-52950232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29647 Neighboring gene uncharacterized LOC124905190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29649

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Novel genes in the PAGE and GAGE family of tumor antigens found by homology walking in the dbEST database. Brinkmann U, et al. Cancer Res, 1999 Apr 1. PMID 10197611
    2. The XAGE family of cancer/testis-associated genes: alignment and expression profile in normal tissues, melanoma lesions and Ewing's sarcoma. Zendman AJ, et al. Int J Cancer, 2002 May 20. PMID 11992404
    3. A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer. Al Olama AA, et al. Nat Genet, 2014 Oct. PMID 25217961, Free PMC Article
    4. Large-scale cDNA transfection screening for genes related to cancer development and progression. Wan D, et al. Proc Natl Acad Sci U S A, 2004 Nov 2. PMID 15498874, Free PMC Article
    5. Development and application of a DNA microarray-based yeast two-hybrid system. Suter B, et al. Nucleic Acids Res, 2013 Feb 1. PMID 23275563, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC71925

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    X antigen family member 3
    Names
    CT12.3
    G antigen, family D, 4
    cancer/testis antigen 12.3
    cancer/testis antigen family 12, member 3a
    cancer/testis antigen family 12, member 3b
    g antigen family D member 4
    placenta-specific 6
    placenta-specific gene 6 protein
    protein XAGE-3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_130776.2 → NP_570132.1  X antigen family member 3

      See identical proteins and their annotated locations for NP_570132.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate exon 1, as compared to variant 1. It thus has a different and shorter 5' UTR, but encodes the same protein as variant 1.
      Source sequence(s)
      AJ318881
      Consensus CDS
      CCDS14347.1
      UniProtKB/Swiss-Prot
      Q5JS82, Q8WTP9, Q8WYS9
      Related
      ENSP00000364640.3, ENST00000375491.7
      Conserved Domains (1) summary
      pfam05831
      Location:1 → 105
      GAGE; GAGE protein

    2. NM_133179.3 → NP_573440.1  X antigen family member 3

      See identical proteins and their annotated locations for NP_573440.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) has an alternate exon 1, as compared to variant 2. It thus has a different and longer 5' UTR, but encodes the same protein as variant 2.
      Source sequence(s)
      AF318372, BC062680
      Consensus CDS
      CCDS14347.1
      UniProtKB/Swiss-Prot
      Q5JS82, Q8WTP9, Q8WYS9
      Related
      ENSP00000303061.3, ENST00000346279.4
      Conserved Domains (1) summary
      pfam05831
      Location:1 → 105
      GAGE; GAGE protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      52862528..52868083 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011530768.3 → XP_011529070.1  X antigen family member 3 isoform X1

      See identical proteins and their annotated locations for XP_011529070.1

      UniProtKB/Swiss-Prot
      Q5JS82, Q8WTP9, Q8WYS9
      Conserved Domains (1) summary
      pfam05831
      Location:1 → 105
      GAGE; GAGE protein

    2. XM_011530769.3 → XP_011529071.1  X antigen family member 3 isoform X1

      See identical proteins and their annotated locations for XP_011529071.1

      UniProtKB/Swiss-Prot
      Q5JS82, Q8WTP9, Q8WYS9
      Conserved Domains (1) summary
      pfam05831
      Location:1 → 105
      GAGE; GAGE protein

    3. XM_011530770.2 → XP_011529072.1  X antigen family member 3 isoform X1

      See identical proteins and their annotated locations for XP_011529072.1

      UniProtKB/Swiss-Prot
      Q5JS82, Q8WTP9, Q8WYS9
      Conserved Domains (1) summary
      pfam05831
      Location:1 → 105
      GAGE; GAGE protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      52147439..52153059 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326599.1 → XP_054182574.1  X antigen family member 3 isoform X1

      UniProtKB/Swiss-Prot
      Q5JS82, Q8WTP9, Q8WYS9

    2. XM_054326597.1 → XP_054182572.1  X antigen family member 3 isoform X1

      UniProtKB/Swiss-Prot
      Q5JS82, Q8WTP9, Q8WYS9

    3. XM_054326598.1 → XP_054182573.1  X antigen family member 3 isoform X1

      UniProtKB/Swiss-Prot
      Q5JS82, Q8WTP9, Q8WYS9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WTP9.1 GenPept UniProtKB/Swiss-Prot:Q8WTP9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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